Phosphinate ester-containing dyes having tunable properties and methods of making the same

A dye having a structure of Formula II or an ionized form thereof:

• wherein R1 is H, a C1-C6 linear or branched alkyl group, azide, alkyne, cyclooctyne, tetrazine, NHS ester, isocyanate, maleimide, iodoacetamide, diazonium salt, DNA-labeling agent, RNA-labeling agent, protein-labeling agent, or a 3-8-membered aryl, heteroaryl, cycloalkyl, or heterocycloalkyl group;
• wherein R2(a) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R2(b);
• wherein R2(b) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, imine, azetidine, or sulfonate, or independently forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R2(a) or R2(c), or forms 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl groups with both R2(a) and R2(c);
• wherein R2(c) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R2(b);
• wherein R3(a) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, azetidine, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R3(b);
• wherein R3(b) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or independently forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R3(a) or R3(c), or forms 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl groups with both R3(a) and R3(c);
• wherein R3(c) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R3(b);
• wherein each R4 is, independently, selected from hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate;
• wherein X is O, N, S, or CH;
• and
• wherein Y is O or S.

A compound having a structure of Formula III or an ionized form thereof:

• wherein R1 is H, a C1-C6 linear or branched alkyl group, azide, alkyne, cyclooctyne, tetrazine, NHS ester, isocyanate, maleimide, iodoacetamide, diazonium salt, DNA-labeling agent, RNA-labeling agent, protein-labeling agent, or a 3-8-membered aryl, heteroaryl, cycloalkyl, or heterocycloalkyl group;
• wherein R2(a) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R2(b);
• wherein R2(b) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, imine, or sulfonate, or independently forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R2(a) or R2(c), or independently forms 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl groups with both R2(a) and R2(c);
• wherein R2(c) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R2(b);
• wherein R3(a) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R3(b);
• wherein R3(b) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or independently forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R3(a) or R3(c), or forms 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl groups with both R3(a) and R3(c);
• wherein R3(c) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R3(b);
• wherein each R4 is, independently, selected from hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate;
• wherein each R5 is, independently, selected from hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, C1-C4 alkoxy, amide, substituted amide, or sulfonate;
• and
• wherein Y is O or S.

A compound having a structure of Formula IV or an ionized form thereof:

• wherein R2(a) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R2(b);
• wherein R2(b) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, imine, or sulfonate, or independently forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R2(a) or R2(c), or independently forms 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl groups with both R2(a) and R2(c);
• wherein R2(c) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R2(b);
• wherein R3(a) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R3(b);
• wherein R3(b) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or independently forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R3(a) or R3(c), or forms 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl groups with both R3(a) and R3(c);
• wherein R3(c) is hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate, or forms a 5- or 6-membered aryl, cycloalkyl, or heterocycloalkyl group with R3(b);
• wherein each R4 is, independently, selected from hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, or sulfonate;
• wherein each R5 is, independently, selected from hydrogen, hydroxyl, a substituted or unsubstituted C1-C4 linear or branched alkyl group, halogen, cyano, isothiocyanate, nitro, azido, substituted or unsubstituted amino, substituted or unsubstituted alkylamino, carboxyl, C1-C4 alkoxy, amide, substituted amide, or sulfonate;
• wherein Y is O or S;
• wherein Z is O, S, substituted or unsubstituted amino, substituted or unsubstituted amide, substituted or unsubstituted alkyl, diazoketone, carboxyl, or a precursor thereof;
• and
• wherein R6 comprises a small molecule.